June 29, 2012

The ceramics probably consisted of simple concave vessels that were likely used for cooking food, said Ofer Bar-Yosef, an archaeologist at Harvard and an author of the study, which appears in the journal Science.

“What it seems is that in China, the making of pottery started 20,000 years ago and never stopped,” he said. “The Chinese kitchen was always based on cooking and steaming; they never made, as in other parts of Asia, breads.”

Science 29 June 2012:

Vol. 336 no. 6089 pp. 1696-1700

DOI: 10.1126/science.1218643

Early Pottery at 20,000 Years Ago in Xianrendong Cave, China

Xiaohong Wu et al.

ABSTRACT

The invention of pottery introduced fundamental shifts in human subsistence practices and sociosymbolic behaviors. Here, we describe the dating of the early pottery from Xianrendong Cave, Jiangxi Province, China, and the micromorphology of the stratigraphic contexts of the pottery sherds and radiocarbon samples. The radiocarbon ages of the archaeological contexts of the earliest sherds are 20,000 to 19,000 calendar years before the present, 2000 to 3000 years older than other pottery found in East Asia and elsewhere. The occupations in the cave demonstrate that pottery was produced by mobile foragers who hunted and gathered during the Late Glacial Maximum. These vessels may have served as cooking devices. The early date shows that pottery was first made and used 10 millennia or more before the emergence of agriculture.

June 28, 2012

A team of scientists, led by researcher Carles Lalueza-Fox from CSIC (Spanish National Research Council), has recovered - for the first time in history - part of the genome of two individuals living in the Mesolithic Period, 7000 years ago. Remains have been found at La Braña-Arintero site, located at Valdelugueros (León), Spain. The study results, published in the Current Biology magazine, indicate that current Iberian populations don't come from these groups genetically.

This appears quite consistent with my model of mostly recent origins of European populations from a West Asian womb of nations. I can't wait to get my hands on this new data.

From the paper:

In the genomic analysis, it is interesting to see that the La Braña individuals do not cluster with modern populations from Southern Europe, including those from the Iberian Peninsula. The first PC separates a north-south distribution, whereas the second follows a general east-west pattern in modern Europeans. The position of La Braña individuals in the 1000 Genomes Project data and the 1KGPomnichip PCAs suggests that the uniform Mesolithic substrate could be related to modern Northern European populations but may represent a gene pool that is no longer present in contemporary Southern European populations. In the latter PCA, where the origin of each Iberian sample is known, it is possible to see that the Mesolithic specimens are not related to modern Basques, contrary to what has been previously suggested in some recent studies [39].

The global PCA of the two individuals shows a clear shift relative to extant Europeans.

So while they are more related to Northern than to Southern Europeans, they are well outside the range of modern European variation. Indeed, there is a strong hint of "Asian-shift" to these individuals. This is completely consistent with the pattern in modern West Eurasian populations. As I noted:

With respect to the Asian- and African- shift of West Eurasian populations, I note that northern Europeans (and Basques) are less African-shifted than southern Europeans, and, at the same time they are more Asian-shifted: the 16 least Asian-shifted populations have a coastline in the Mediterranean (excluding the Portuguese), while the 16 least African-shifted populations do not (excluding the French).

It now appears clear that the Mesolithic substratum in Europe was:

Well outside the modern range, contributing a little to extant populations

Its contribution in northern populations was higher than in southern ones

It may be responsible for the pattern of Asian-shift observed for non-Mediterranean European populations

UPDATE: Due to the small number of SNPs, I pooled the two Mesolithic individuals into a single composite one; the K7b admixture proportions are: 9.3% African and 90.7% Atlantic_Baltic, which appears consistent with the position of the individuals in the European PCA plot. The sub-1,000 SNPs in common with the K7b do not give me a lot of confidence in the minority element, but, in any case, the high Atlantic_Baltic figure is what I would expect and appears consistent with the similarly high Atlantic_Baltic figure of the Swedish Neolithic hunter-gatherers.

Summary
The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic [1,2,3,4,5,6,7,8,9,10] is poorly understood, both due to the scarcity of human remains from that period [11,12,13,14,15,16,17,18] and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns [19,20,21,22]. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain) [23]. The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

Junior researcher Zuzana Fajkošová passes international selection procedure and begins her doctorate in the Palaeogenetics Group at the JGU Institute of Anthropology

27.06.2012

"BEAN – Bridging the European and Anatolian Neolithic" is the name of a new multinational educational network which has received funding from the European Commission for the next four years. It is classified as a so-called Initial Training Network (ITN) in the EU Marie Curie Actions program, which allows young scientists early access to research activity at top international institutions. A basic requirement for funding is that the researchers involved leave their home country and conduct their research in another European country.

The BEAN Network consists of several European partners in England, Switzerland, France, Germany, Serbia, and Turkey, and has set itself the goal of enhancing the skills of a new generation of researchers in the subjects of anthropology, pre-history, population genetics, computer modeling, and demography. Many different disciplines are participating in the initiative. An important associate partner on the German side is the German Federal Statistical Office in Wiesbaden. The common focus of the project partners centers around questions associated with the origin of first farmer settlements, which were established some 8,000 years ago in West Anatolia and the Balkans. Where did they come from? Were they migrants from the Middle East? Are they our ancestors?

Anthropologists at Johannes Gutenberg University Mainz (JGU) have been meticulous in their preparation of the project over the last years and have entered into various cooperations to underpin it. Seven research institutions and two commercial companies are now working together on the BEAN project. Two leading researchers serve the network in an advisory capacity. These are archaeologist Ian Hodder from Stanford, who established his reputation with his excavations in Catal Höyük, and Hermann Parzinger, President of the Prussian Cultural History Foundation, who spent many years excavating and researching in European Turkey.

As of July 2012, doctoral candidate Zuzana Fajkošová, who completed her undergraduate studies at Masaryk University in Brno and at Charles University in Prague in the Czech Republic, will be the first of two BEAN researchers to start work at JGU's Institute of Anthropology and in the new palaeogenetic laboratory, which is currently in the final stages of construction on the edges of the university's Botanic Garden. She will analyze DNA from the bones of the last hunter-gatherers and the first settled farmers in the region between West Anatolia and the Balkans using the new cutting-edge technology of Next Generation Sequencing (NGS). Together with her colleagues in Dublin, London, and Geneva, she will use the genomic data to compile a model for the settlement of Europe.

"It is both a great honor and a huge opportunity for me that I can work together with such renowned researchers. I'm looking forward to Mainz, the university and the institute's new building," comments Fajkošová, who turned down a number of other offers in order to work at JGU. "A major factor leading to her appointment was the fact that besides mastering biomolecular techniques she also has good programming skills,” explains Professor Dr. Joachim Burger, the Network Coordinator. "A few years ago we more or less founded the discipline of Neolithic Palaeogenetics single-handedly. However, undertaking genomic projects is possible only with the help of international colleagues. That is why we are so pleased that such networks give us and our colleagues the chance to train young research talents."

Besides academic training, the young researchers will be able to do practical work for the two commercial companies within the network and thereby gain work experience in a non-university environment. "This is important as not all of the candidates will opt for a pure research career," explains Karola Kirsanow, who moved from Harvard to Mainz last year and now administrates the network together with Burger. "Our young colleagues have to attend many workshops, courses, and internships, most of them abroad. While this makes for a very tough program, we believe that it significantly enhances the quality of the training and similarly enhances candidates' career prospects."

The recent publication of Omberg et al. (2012) has reminded me of the data of Henn et al. (2012) on Qatar which I don't believe I've used yet. I used the K12b calculator on ~20,000 SNPs that are common between it and the Affymetrix chip used.

Below is the population portrait of the Qatari population:

Obviously this isn't a homogeneous population. In order to figure out which ancestral groups are present there, I ran MCLUST over the admixture proportions, which resulted in individuals assigned to five different clusters. Here are the average admixture proportions of these five clusters:

On the basis of the above, I conclude that there are several different groups represented in the Qatari population. I have absolutely no knowledge about the Qatari population, so it would be interesting to see if readers find correspondences between these and known social divisions in Qatar.

For example, I could wager that #5 which is a "Southwest Asian"+"Caucasus" mix represents a pure Arabian group with little outside influences. #1 and #2 are also Arab-like but with various degrees of admixture. #3 appears to include substantial African descendants and #4 a clear Iranian signal due to the high "Gedrosia" component. Of interest is that the "African" group #3 also scores high in the "South Asian" component.

Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. 1

Results

Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information.

Conclusions

By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

Evolutionary history of continental South East Asians: “early train” hypothesis based on genetic analysis of mitochondrial and autosomal DNA data

Timothy A. Jinam et al.

The population history of the indigenous populations in island Southeast Asia is generally accepted to have been shaped by two major migrations; the ancient ‘Out of Africa’ migration ∼50,000 years before present (YBP) and the relatively recent ‘Out of Taiwan’ expansion of Austronesian agriculturalists approximately 5,000 YBP. The Negritos are believed to have originated from the ancient migration whereas the majority of island Southeast Asians are associated with the Austronesian expansion. We determined 86 mitochondrial DNA (mtDNA) complete genome sequences in four indigenous Malaysian populations, together with a reanalysis of published autosomal single nucleotide polymorphism (SNP) data of Southeast Asians to test the plausibility and impact of those migration models. The three Austronesian groups (Bidayuh, Selatar and Temuan) showed high frequencies of mtDNA haplogroups which originated from the Asian mainland ∼30,000 to 10,000 YBP while showing low frequencies of ‘Out of Taiwan’ markers. Principal Component Analysis and phylogenetic analysis using autosomal SNP data indicate a dichotomy between continental and island Austronesian groups. We argue that both the mtDNA and autosomal data suggest an ‘Early Train’ migration originating from Indochina or South China around the late-Pleistocene to early Holocene period which predates, but may not necessarily exclude, the Austronesian expansion.

The mitochondrial DNA (mtDNA) still remains an
important marker in the study of human history, especially if considering the increasing amount of data
available. Among the several questions regarding human history that are under debate, the model of expansion of
agriculture into Europe from its source in the Near East is still unclear. Recent
studies have indicated that clusters
belonging to haplogroup K, a major clade from U8, might be related with the Neolithic expansions. Therefore, it is crucial
to identify the founder lineages of the Neolithic in Europe so that we may understand the real genetic input of the first
Near Eastern farmers in the current European population and comprehend how agriculture spread so quickly throughout
all Europe. In order to achieve this
goal, a total of 55 U8 samples from the Near East, Europe and North Africa were
selected for complete characterisation
of mtDNA. A maximum-parsimonious phylogenetic tree was constructed using all
published sequences available so far.
Coalescence ages of specific clades were estimated using ρ statistic, maximum likelihood and Bayesian methods considering a mutation
rate for the complete molecule corrected for purifying selection. Our
results show that U8 dates to ~37-54 thousand years ago (ka) suggesting that
this haplogroup might have been carried
by the first modern humans to arrive in Europe,
~50 ka. Haplogroup K most likely originated in the Near
East ~23-32 ka where it
might have remained during the Last Glacial Maximum, between 26-19 years ago. The
majority of K subclades date to the Late
Glacial and are related with the repopulation of Europe
from the southern refugia areas. Only a
few lineages appear to reflect post glacial, Neolithic or post-Neolithic
expansions, mostly occurring within Europe. The
major part of the lineages dating to the
Neolithic period seems to have an European origin with exception of haplogroup K1a4 and K1a3. Clade K1a4 appears to be
originated from the Near East where it also
reaches its highest peak of diversity. Despite
the main clades of K1a4 arose in the Near East during the Late Glacial, its
subclade K1a4a1 dates to ~9-11 ka and is
most likely related with the Neolithic dispersal to Europe. Similarly, K1a3
probably originated in the Near East
during the Late Glacial and its subclade K1a1a dispersed into Europe ~11-13 ka
alongside with the expansion of agriculture.

Late
Glacial Expansions in Europe revealed through
the fine-resolution characterisation of mtDNA haplogroup U8

The maternally inherited and fast evolving
mitochondrial DNA (mtDNA) molecule is a highly informative tool with which to reconstruct human prehistory. This has
become even more true in recent years, as mtDNA based studies are becoming more robust and powerful due to the
availability of complete mtDNA genomes. These allow better mutation rate estimates and fine-resolution
characterisation of the phylogeography of mtDNA haplogroups, or named clades.
MtDNA haplogroup K, the major subclade of U8, occurs at low frequencies
through West Eurasian populations, and
is much more common in Ashkenazi Jews. However, the lack of variation on the
first hypervariable segment (HVSI) has precluded any meaningful phylogeographic
analysis to date. We therefore completely sequenced 50 haplogroup K and 5 non-K U8 mtDNA samples from across
Europe and the Near East, and combined them with 343 genomes previously deposited in GenBank, in order to
reconstruct a detailed phylogenetic tree. By combining several inference methods, including maximum parsimony, maximum
likelihood and Bayesian inference it was possible to trace the timescale and geography of the main expansions
and dispersals associated with this lineage. We confirmed that haplogroup K, dating to ~32 thousand years
(ka) ago, descended from the U8 clade, which coalesces ~48 ka ago. The latter is close to the timing of the first
arrival of modern humans in Europe and U8 could be one of the few surviving mtDNA lineages brought by the first settlers
from the Near East. U8 split into the widespread U8b, at ~43 ka, and U8a, which seems to have expanded only in Europe
~24 ka ago. Considering the pattern of diversity and the geographic distribution, haplogroup K is most likely to
have arisen in the Near East, ~32 ka ago. However, some subclades were evidently carried to Europe during the Last
Glacial Maximum (LGM). We observed significant expansions of haplogroup K lineages in the Late Glacial period (14-19
ka), reflecting expansions out of refuge areas in southwest and possibly also southeast Europe.

The past 15 years have witnessed a notable scientific interest in the topic of
crop domestication and the emergence of agriculture
in the Near East. Multi-disciplinary
approaches brought a significant amount of new data and a multitude of hypotheses and interpretations. However, some
seemingly conflicting evidence, especially in the case of emmer wheat, caused certain controversy and a broad
scientific consensus on the circumstances of the wheat domestication has not been reached, yet. The past phylogenetic research has translated
the issue of wheat domestication into somewhat simplistic mono- /polyphyletic
dilemma, where the monophyletic origin of a crop signalizes rapid and
geographically localized domestication,
while the polyphyletic evidence suggests independent, geographically separated
domestication events. Interestingly, the
genome-wide and haplotypic data analyzed in several studies did not yield
consistent results and the proposed
scenarios are usually in conflict with the archaeological evidence of lengthy
domestication. Here I suggest that the
main cause of the above mentioned inconsistencies might lie in the inadequacy
of the divergent, tree-like evolutional
model. The inconsistent phylogenetic results and implicit archaeological
evidence indicate a reticulate (rather
than divergent) origin of domesticated emmer. Reticulated genealogy cannot be
properly represented on a phylogenetic
tree; hence different sets of samples and genetic loci are prone to conclude
different domestication scenarios. On a
genome-wide super-tree, the conflicting phylogenetic signals are suppressed and
the origin of domesticated crop may
appear monophyletic, leading to misinterpretations of the circumstances of the
Neolithic transition. The network analysis of multi-locus sequence
data available for tetraploid wheat clearly supports the reticulated origin of domesticated emmer and durum wheat. The
concept of reticulated genealogy of domesticated wheat sheds new light onto the emergence of Near-Eastern agriculture
and is in agreement with current archaeological evidence of protracted and dispersed emmer domestication.

In
addition to their distinctive subsistence patterns, African hunter-gatherers
belong to some of the most genetically diverse
populations on Earth. To infer
demographic history and detect signatures of natural selection, we sequenced the whole genomes of five individuals in each
of three geographically and linguistically diverse African hunter-gatherer populations at >60x coverage. In these 15 genomes we identify 13.4 million
variants, many of which are novel, substantially
increasing the set of known human variation.
These variants result in allele frequency distributions that are free of SNP ascertainment bias. This genetic data is used to infer
population divergence times and demographic history (including population bottlenecks and
inbreeding). We find that natural
selection continues to shape the genomes of hunter-gatherers, and that deleterious genetic
variation is found at similar levels for hunter-gatherers and African populations with agricultural or pastoral
subsistence patterns. In addition, the
genomes of each hunter-gatherer population
contain unique signatures of local adaptation.
These highly-divergent genomic regions include genes involved in immunity, metabolism, olfactory and taste perception,
reproduction, and wound healing.

The Caribbean region has a rich cultural and biological diversity,
including several countries with different languages, and important historical events like the
arrival of the Europeans in the late fifteenth century affected it deeply. Although
it has been said that two main Native
American groups peopled the Caribbean at the time of Columbus’s voyages—the Arawakan-speaking Tainos and the Caribs—this
model has been questioned because it comes from the descriptions written by the conquerors. The archaeological
record shows a richer picture of trade among the islands, cultural change and diversity than what colonial documents
depict, from the early settlements around 8000 B.P. to the chiefdoms and towns at the time of contact. How this area
was peopled and how its inhabitants interacted with the surrounding continent are questions that remain to be
answered due to the fragmentary nature of the historical and archaeological records.
We aim to reconstruct the Native
American genetic diversity from the time of the Spanish arrival at the island
of Puerto Rico from its contemporary
population. We seek to find out how the original peopling of Puerto Rico
occurred, along with which contemporary
Native American populations are the most closely related to the Native tracks
found. We used PCAdmix to trace Native
American segments in admixed individuals, thus enabling us to reconstruct the
original native lineages previous to the
European and African contact.

Specifically,
we generated local ancestry calls for the 70 parents of the 35 complete Puerto
Rican trios from the wholegenome and Illumina Omni 2.5M chip Genotype data of
the 1000 Genomes Project, both to examine genome-wide admixture patterns and to infer demographic
historical events from ancestry tract length distributions and an
ancestryspecific PCA approach, adding 55 Native American groups as potential
source populations (N=475 genotyped through Illumina’s 650K array) and 15 selected Mexican
trios (genotyped on Affymetrix’s 6.0 array, including about 906,000 SNPs) to provide population context. ADMIXTURE
analysis has shown that in Puerto Rico there is no single source of contribution for the Native component. Rather,
this component seems to include a mixture of major Mexican and Andean components with little contributions
from the Amazonian isolates. On the other hand, the ancestry-specific PCA plotted the Puerto Rican Native segments
tightly clustered with the Native segments of groups from the same language family as the Tainos (Equatorial-Tucanoan),
showing a clear association between linguistics and genetics instead of a geographical one.

Inference of demographic history and natural selection in African Pygmy populations from whole-genomesequencing data

The
Pygmy populations of Central Africa are some of the last remaining
hunter-gatherers among present-day human populations, and can be broadly classified
into two geographically separated groups, the Western and Eastern Pygmies. Compared to their neighboring populations of
predominantly Bantu origin, Pygmy populations show distinct cultural and physical characteristics, most notably short
stature, often referred to as the “Pygmy phenotype”. Given their distinct physical characteristics, the questions of the
demographic history and origin of the Pygmy phenotype have attracted much attention. Previous studies have shown an
ancient divergence (~60,000 years ago) of the ancestors of modernday Pygmies
from non-Pygmies, and a more recent split of the Eastern and Western Pygmy
groups. However, these studies were
generally based on a relatively small set of markers, precluding accurate
estimations of demographic parameters.
Furthermore, despite the considerable interest, to date there is still little
known about the genetic basis of the
small stature phenotype of Pygmy populations.

In order to address these questions, we sequenced
the genomes of 47 individuals from three populations: 20 Baka, a Pygmy hunter-gatherer population from the
Western subgroup of the African Pygmies; 20 Nzebi, a neighboring nonPygmy
agriculturist population from the Bantu ethnolinguistic group; as well as 7
Mbuti, Eastern Pygmy population, from the
Human Genome Diversity Project (HGDP). We performed whole-genome sequencing
using Illumina Hi-Seq 2000 to a median
sequencing depth of 5.5x per individual. After stringent quality control
filters, we call over 17 Million SNPs across
the three populations, 32% of them novel (relative to dbSNP 132). Genotype
accuracy after imputation was assessed
using genotype data from the Illumina OMNI1 SNP array, and error rates were
found to be comparable to other
low-coverage studies (< 3% for most individuals). Preliminary results show
relatively low genetic differentiation between
the Baka and the Nzebi (mean FST = 0.026), whereas the Mbuti show higher
differentiation to both Baka and Nzebi
(mean FST = 0.060 and 0.070, respectively). Furthermore, we find that alleles
previously found to be associated with height in other populations are not
enriched for the “small” alleles in the Pygmy populations. We find a number of highly differentiated genomic regions as candidate
loci for height differentiation, which will be verified using simulations under the best-fit demographic model, inferred
from multi-dimensional allele frequency spectra using DaDi. Our dataset will allow a detailed investigation of the
demographic history and the genomics of adaptation in these populations.

Genetic
structure in North African human populations and the gene flow to Southern Europe

Laura R
Botigué 1 , Brenna M Henn 2 , Simon Gravel 2 , Jaume Bertranpetit 1 , Carlos D
Bustamante 2 , David Comas 1 1 Institut de Biologia Evolutiva (IBE, CSIC-UPF),
Barcelona, Spain, 2 Stanford University,
Stanford CA, USADespite
being in the African continent and at the shores of the Mediterranean,
North African populations might have experienced
a different population history compared to their neighbours. However, the
extent of their genetic divergence and
gene flow from neighbouring populations is poorly understood. In order to
establish the genetic structure of North Africans and the gene flow with the Near East,
Europe and sub-Saharan Africa, a genomewide
SNP genotyping array data (730,000
sites) from several North African and Spanish populations were analysed and
compared to a set of African, European
and Middle Eastern samples. We identify a complex pattern of autochthonous,
European, Near Eastern, and sub-Saharan
components in extant North African populations; where the autochthonous
component diverged from the European and
Near Eastern component more than 12,000 years ago, pointing to a pre-Neolithic ‘‘back-to-Africa’’ gene flow. To estimate the
time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method
based on the frequency and length distribution of migrant tracts, which has suggested a migration of western African
origin into Morocco ~1,200 years ago and a migration of individuals with Nilotic ancestry into Egypt ~ 750 years ago. We characterize broad patterns of recent gene
flow between Europe and Africa, with a gradient of recent African ancestry that is highest in southwestern Europe and decreases in northern latitudes. The elevated
shared African ancestry in SW Europe (up to 20% of the individuals’ genomes) can be
traced to populations in the North African Maghreb. Our results, based on both
allele-frequencies and shared haplotypes, demonstrate that recent migrations
from North Africa substantially
contribute to the higher genetic diversity in southwestern Europe

Estimating
a date of mixture of ancestral South Asian populations

Priya
Moorjani 1,2 , Nick Patterson 2 , Periasamy Govindaraj 3 , Danish Saleheen 4 ,
John Danesh 4 , Lalji Singh* 3,5 , Kumarasamy
Thangaraj* 3 , David Reich* 1,2 1 Harvard University, Boston, Massachusetts,
USA, 2 Broad Institute, Cambridge,
Massachusetts, USA, 3 Centre for Cellular and Molecular Biology, Hyderabad,
Andhra Pradesh, India, 4 Dept of Public
Health and Care, University of Cambridge,
Cambridge, UK, 5 Genome Foundation,
Hyderabad, Andhra Pradesh, IndiaLinguistic
and genetic studies have demonstrated that almost all groups in South Asia today descend from a mixture of two highly divergent populations: Ancestral
North Indians (ANI) related to Central Asians, Middle Easterners and Europeans, and Ancestral South Indians (ASI)
not related to any populations outside the Indian subcontinent. ANI and ASI have been estimated to have diverged from
a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown. Here we analyze
data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some
mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is
universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all
caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred within the last four thousand years,
a cultural shift led to widespread endogamy, decreasing the rate of additional mixture.

Long IBD in
Europeans and recent population history

Peter Ralph, Graham Coop UC Davis, Davis, CA, USA

Numbers of common ancestors
shared at various points in time across populations can tell us about recent demography,
migration, and population movements. These
rates of shared ancestry over tens of generations can be inferred from genomic data, thereby dramatically increasing
our ability to infer population history
much more recent than was previously possible with population genetic techniques.We have analyzed patterns of IBD in a dataset of thousands of Europeans from across the continent, which
provide a window into recent European
geographic structure and migration.

Gene flow
between human populations during the exodus from Africa,
and the timeline of recent human evolution

We present a novel test for historical
gene flow between populations using unphased genotypes in present-day individuals, based on the sharing of derived
alleles and making a minimal set of assumptions about their demographic history. We apply this test to data for three
human individuals of African, European and Asian ancestry. We find that the joint distribution of European and Asian
genotypes is compatible with these populations having separated cleanly at some time in the past without subsequent
genetic exchange. However the same is not true of the European-African and Asian-African distributions, which instead
suggest an extended period of continued exchange between African and nonAfrican
populations after their initial separation.

We discuss this in comparison with
recent models and estimates of separation time between these populations. We also consider the impact of recent direct
experimental studies of the human mutation rate, which suggest rates of around 0.5 × 10 -9 bp -1 y
-1 , substantially lower than prior estimates of 1 × 10 -9 bp -1 y
-1 obtained from calibration against the primate fossil record. We show that in
several places the lower rate, implying older dates, yields better agreement between genetic and non-genetic
(paleoanthropological and archaeological) evidence for events surrounding the exodus of modern humans from Africa
and their dispersion worldwide.

A long-standing goal in population genetics is to unravel the relative importance of evolutionary forces that shape genetic diversity. Here we focus on human populations in Central Asia, a region that has long been known to contain the highest genetic diversity on the Eurasian continent. However, whether this variation principally reflects long-term presence, or rather the result of admixture associated with repeated migrations into this region in more recent historical times, remains unclear. Here we investigate the underlying demographic history of Central Asian populations in explicit relation to Western Europe, Eastern Asia and the Middle East. For this purpose we employ both full Bayesian and approximate-Bayesian analyses of nuclear genetic diversity in 20 unlinked non-coding resequenced DNA regions, known to be at least 200 kb apart from any known gene, mRNA or spliced EST (total length of 24 kb), and 22 unlinked microsatellite loci.

Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians) with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications that this region might have genetically influenced Western European populations, rather than vice versa. A further evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both long-term presence and admixture in more recent historical times.

Population
structure and evidence of selection in the Khoe-San and Coloured populations
from southern Africa

The San and Khoe people currently represent remnant groups of a
much larger and widely distributed population of hunter-gatherers and pastoralists who had
exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne
immigrants within the last 350 years. Mitochondrial DNA, Y-chromosome and autosomal studies conducted on a few San
groups revealed that they harbour some of the most divergent lineages found in living peoples throughout the world.

We used autosomal data to characterize
patterns of genetic variation among southern African individuals in order to understand human evolutionary history, in
particular the demographic history of Africa. To
this end, we successfully genotyped ~
2.3 million genome wide SNP markers in 220 individuals, comprising seven
Khoe-San, two Coloured and two
Bantu-speaking groups from southern Africa. After quality filtering, the data
were combined with publicly available SNP
data from other African populations to investigate stratification and
demography of African populations.

We also applied a newly developed method of estimating
population topology and divergence times. Genotypes and inferred haplotypes were used to assess genetic
diversity, patterns of haplotype variation and linkage disequilibrium in
different populations. We found that six of the seven Khoe-San populations
form a common population lineage basal to all other modern human populations. The studied Khoe-San
populations are genetically distinct, with diverse histories of gene flow with surrounding populations. A clear geographic
structuring among Khoe-San groups was observed, the northern and southern Khoe-San groups were most distinct
from each other with the central Khoe-San group being intermediate. The Khwe group contained variation that
distinguished it from other Khoe-San groups. Population divergence within the Khoe-San group is approximately 1/3 as ancient
as the divergence of the Khoe-San as a whole to other human populations (on the same order as the time of
divergence between West Africans and Eurasians). Genetic diversity in some, but not all, Khoe-San populations is
among the highest worldwide, but it is influenced by recent admixture. We furthermore find evidence of a Nilo-Saharan
ancestral component in certain Khoe-San groups, possibly related to the introduction of pastoralism to southern
Africa.

We searched for signatures of
selection in the different population groups by scanning for differentiated
genome-regions between populations and
scanning for extended runs of haplotype homozygosity within populations. By
means of the selection scans, we found
evidence for diverse adaptations in groups with different demographic histories
and modes of subsistence.

Impacts of
life-style on human evolutionary history: A genome-wide comparison of herder
and farmer populations in Central Asia

Kyrgyzstan Human
populations use a variety of subsistence strategies to exploit an exceptionally
broad range of habitats and dietary
components. These aspects of human environments have changed dramatically
during human evolution, giving rise to
new selective pressures. Here we focused on two populations in Central Asia
with long-term contrasted lifestyles: Kyrgyz’s
that are traditionally nomadic herders, with a traditional diet based on meat
and milk products, and Tajiks that are
traditionally agriculturalists, with a traditional diet based mostly on
cereals. We genotyped 93 individuals for more than 600,000 SNP markers (Human-660W-Quad-V1.0
from Illumina) spread across the genome. We first analysed the population structure of these two populations
in the world-wide context by combining our results with other available genome-wide data. Principal component and
Bayesian clustering analyses revealed that Tajiks and Kirgiz’s are both admixed populations which differed however
from each other with respect to their ancestry proportions: Tajiks display a much larger proportion of common ancestry with
European populations while Kirgiz’s share a larger common ancestry with Asiatic populations. We then examined the
region of the genome displaying unusual population differentiation between these two populations to detect
natural selection and checked whether they were specific to Central Asia or not. We complemented these analyses with
haplotype-based analyses of selection.

Bayesian
inference of the demographic history of Niger-Congo speaking populations

The Niger-Congo phylum encompasses more than 1500 languages spread
over sub-Saharan Africa. This current wide range is mostly due to the spread of
Bantu-speaking people across sub-equatorial regions in the last 4000-5000
years. Although several genetic studies
have focused on the evolutionary history of Bantu-speaking groups, much less
effort has been put into the
relationship between Bantu and non-Bantu Niger-Congo groups. Additionally,
archaeological and linguistic evidence
suggest that the spread of these populations occurred in distinct directions
from the core region located in what is
now the border between Nigeria
and Cameroon towards West
and South Africa,
respectively. We have performed
coalescent simulations within an approximate Bayesian computation (ABC)
framework in order to statistically
evaluate the relative probability of alternative models of the spread of
Niger-Congo speakers and to infer demographic
parameters underlying these important migration events. We have analysed 61
high-quality microsatellite markers,
genotyped in 130 individuals from three Bantu and three non Bantu-speaking
populations, representing a "Southern
wave" or the Bantu expansion, and a "Western wave",
respectively. Preliminary results suggest that models inspired by a spatial spread of the
populations are better supported than classical isolation with migration (IM)
models. We also find that Niger-Congo
populations currently maintain high levels of gene flow with their neighbours,
and that they expanded from a single
source between 200 and 600 generations, even though available genetic data do
not provide enough information to
accurately infer these demographic parameters.

Human skin colour is a polygenic trait that is primarily determined by the amount and type of melanin produced in the skin. The pigmentation variation between human populations across the world is highly correlated with geographic latitude and the amount of UV radiation. Association studies together with research involving different model organisms and coat colour variation have largely contributed to the identification of more than 378 pigmentation candidate genes. These include TYR OCA2, that are known to cause albinism, MC1R responsible for the red hair phenotype, and genes such as MATP, SLC24A5 and ASIP that are involved in normal pigmentation variation. In particular, SLC24A5 has been shown to explain one third of the pigmentation difference between Europeans and Africans. However, the same gene cannot explain the lighter East Asian phenotype; therefore, light pigmentation could be the result of convergent evolution. A study on UK residents of Pakistani, Indian and Bangladeshi descent found significant association of SLC24A5, SLC45A2 and TYR genes with skin colour. While these genes may explain a significant proportion of interethnic differences in skin colour, it is not clear how much variation such genes explain within Indian populations who are known for their high level of diversity of pigmentation. We have tested 15 candidate SNPs for association with melanin index in a large sample of 1300 individuals, from three related castes native to South India. Using logistic regression model we found that SLC24A5 functional SNP, rs1426654, is strongly associated with pigmentation in our sample and explains alone more than half of the skin colour difference between the light and the dark group of individuals. Conversely, the other tested SNPs fail to show any significance; this strongly argues in favour of one gene having a major effect on skin pigmentation within ethnic groups of South India, with other genes having small additional effects on this trait. We genotyped the SLC24A5 variant in over 40 populations across India and found that latitudinal differences alone cannot explain its frequency patterns in the subcontinent. Key questions arising from this research are when and where did the light skin variant enter South Asia and the manner and reason for it spreading across the Indian sub-continent. Hence, a comprehensive view of skin colour evolution requires that in depth sequence information be corroborated with population (genetic) history and with ancient DNA data of past populations of Eurasia.

Reconstructing
demographic histories from long tracts of DNA sequence identity

Kelley Harris 1
, Rasmus Nielsen 1,2 1 UC Berkeley, Berkeley, CA, USA, 2 University of Copenhagen, Copenhagen,
Denmark There has been recent excitement and debate about the details of human
demographic history, involving gene flow that has occurred between populations as well as
the extent and timing of bottlenecks and periods of population growth. Much of the debate concerns the timing of past
admixture events; for example, whether Neanderthals exchanged genetic material with the ancestors of
non-Africans before before or after they left Africa.
Here, we present a method for using
sequence data to jointly estimate the timing and magnitude of past genetic
exchanges, along with population divergence
times and changes in effective population size. To achieve this, we look at the
length distribution of regions that are
shared identical by state (IBS) and maximize an analytic composite likelihood
that we derive from the sequentially
Markov coalescent (SMC). Recent gene flow between populations leaves behind
long tracts of identity by descent
(IBD), and these tracts give our method its power by influencing the
distribution of shared IBS tracts. However, since IBS tracts are directly observable, we
do not need to infer the precise locations of IBD tracts. In this way, we can accurately estimate admixture times for
relatively ancient events where admixture mapping is not possible, and in simulated data we show excellent power to
characterize admixture pulses that occurred 100 to several hundred generations ago. When we study the IBS tracts
shared between and within the populations sequenced by the 1000 Genomes consortium, we find evidence that
there was no significant gene flow between Europeans and Asians within the past few hundred generations. It also
looks unlikely that the Yorubans of Nigeria interbred with Europeans or Asians in a population-specific way, though there may
have been admixture between Africans and an ancestral non-African population.

Which way did they go? Detecting directional migration from genetic data

Range expansions and colonizations are ubiquitous in many species and are studied from many different perspectives in e.g. anthropology, biogeography and invasion biology. It has been well established that these colonization events lead to a loss of genetic diversity and that in many cases it is possible to infer the history of a species' range from present-day genetic data. Previous approaches were mainly based on within-population measures of diversity such as heterozygosity, which then have been compared between populations. However, it is also well established that these statistics are susceptible to confounding demographic factors such as unequal subpopulation sizes or population size changes. In this study, we propose a novel method using data from multiple populations to infer a population's history. Our approach is based on a statistic that detects asymmetries in the 2D-allele frequency spectrum that occur when one population consists mostly of offspring of another population, as we expect in an expanding population. We show that our statistic is able to detect the direction of an expansion using data from multiple populations. Using simulations, we further show that our statistic is generally more powerful than previous approaches and that it is robust to a wide array of confounding demographic factors. We further illustrate the use of our statistic on several data sets for humans, Drosophila and Neurospora and show that we are both able to detect global patterns of colonization and fine-scale population structure.

About 11,000 years ago, a change in human lifestyle took place in the territories of present-day western Iran, the Levant region and south-east Anatolia, which is characterised particularly by four factors: the people founded permanent settlements with buildings for various functions; plants such as Einkorn and beans were cultivated; goats, sheep, pigs and cattle were domesticated; a new kind of culture evolved, that became conspicuous with the appearance of a new material culture including ground stone tools and later, pottery products. The transition from the partly nomadic huntergatherer subsistence strategy to a settled lifestyle based on food production is also known as the “Neolithic Revolution”. About 8,500 years ago, the Neolithic culture spread to the southeast of Europe and later expanded episodically across central and northern Europe. The extent to which this movement of a farming culture was accompanied by a movement of people, as opposed to just a spread of ideas and skills, has been a subject of considerable debate and dispute over the last 100 years. Population genetic computer simulations of genetic data from ancient human remains, based on coalescent theory have shown that the early Neolithic farmers could not have been descended just from the later hunter-gatherers of central Europe (Bramanti et al. 2009). As the hunter-gatherers had already been settled in Central Europe since the retreat of the glaciers 20 kya, Neolithic famers must have migrated into this area.

There is good evidence of cultural contact between hunter-gatherers and early farmers in central Europe. Whether the exchange of hunting tools also led also to the exchange of men is still not clear, as Y-chromosomal DNA has not yet been studied systematically in ancient human remains. Moreover, ancient DNA evidence is now emerging that other regions don/t follow the patterns of population discontinuity observed in Central Europe. While the overall results support a model of demic diffusion of farmers from southeastern Europe, or even further East, in to Central Europe, it is very likely that modern populations in most parts of Europe were formed by varying degrees of admixture between incoming farmers and indigenous hunter-gatherers. Analyses of the appropriate neutral and phenotypically informative markers using next generation sequencing technologies will provide more information on this in the near future.

Population genetic properties of time serial data with examples from ancient population-genomic data

Mattias Jakobsson Uppsala University, Uppsala, Sweden

Extracting genetic information from ancient material has for long been hampered by numerous difficulties since its first steps some two decades ago, but in the last few years, many of these problems have been solved and the use of ancient DNA (aDNA) is now beginning to show its full potential. We will likely see a wealth of genomic data from ancient populations, but the statistical properties of time-structured genetic samples are considerably less explored than population genetic patterns arising from spatial structure. Using simulations, we explore and highlight features of temporal structure and spatial structure, such as an 'isolation-by-time' effect that is similar to isolation-by-distance. Using model- and simulation-based approaches, we can now make novel inferences about demographic and evolutionary questions from time serial data. We will discuss examples from the long standing debate about the introduction of farming in Europe and question about archaic ancestry in East Asia using paleogenomic data.

The geographical and temporal
origin of the dog is controversial. Genetic data suggest a domestication event
in Asia or the Middle East about 15,000
- 30,000 years ago, whereas the oldest dog-like fossils are found in Europe dating to over 30 thousand years ago. We genetically analyzed
the remains of 14 prehistoric wolves and dogs including some of the oldest dog remains described from the New and Old World. Utilizing array based DNA capture techniques
coupled with Illumina double indexed
sequencing, we targeted a total of ~750,000 nucleotides in each of the ancient
canids and additional 20 contemporary
wolves from North America and Eurasia. The
sequence information comprised the complete mitochondrial genome, 3,000 SNPs previously
identified as highly informative for differentiating dogs from wolves, exonic sequences from 62 potential
domestication genes and ~150,000 nucleotides of non-coding regions spread throughout the genome. Initial
analyses reveal that we have successfully captured and sequenced the complete
mitochondrial genome with high coverage
as wells as a substantial number of autosomal fragments from ten prehistoric
canids and all contemporary wolves.
Phylogenetic analysis combining the complete mitochondrial genomes of the
prehistoric canids with those of a large
collection of modern dogs and wolves result in a statistically well supported
tree. While some haplotypes cluster within
modern dogs or wolves, others show a basal placement in the phylogeny. The
latter finding might support a previous
notion that an aberrant lineage of dog-like canids might have existed
throughout the northern hemisphere during
the late Pleistocene and became globally extinct during the last 20,000 years. We
will test this hypothesis by investigating
the autosomal loci and employ sophisticated phylogenetic analyses, demographic
modeling and selection scans to better
understand the influence of early human society and artificial selection on the
canine genome.

Admixed human genomes reveal complex demographic patterns from early modern humans to the contemporary era

A substantial proportion of humans are "admixed", in the sense that their recent ancestors belong to statistically distinct groups. This needs to be accounted for if unbiased inference and associations are to be performed. We present a diversity of methods for the analysis of whole-genome sequence data from admixed individuals, and apply them to 50 genomes sequenced by Complete Genomics, including 4 Mexican-Americans, 4 African-Americans and 2 individuals from Puerto Rico, together with SNP genotype data from hundreds of additional samples.

Many methods have been presented recently to infer the population of origin of specific loci along the genomes of admixed individuals, leading to inferred mosaics of ancestry. We first propose a simple Markov model that relates the time-dependent migration history to the inferred patterns of local ancestry. We use this framework to infer the timing of admixture and to differentiate between punctual and continuous models of migration: using demographic models that are consistent with both historical records and genetic data, we find evidence for continuous migration patterns in both Mexican and African-American populations.

We also propose models to study the longer-term evolution of the ancestral populations, by considering the allele frequency distribution, pairwise TMRCA's, and a simple extension of the recently introduced Pairwise Sequentially Markovian Coalescent approach for demographic inference. The inferred source population demographic histories are in broad agreement with previous results for European and West-African populations, and the inferred demography for the Native source population closely follows the European one until about 20,000 years ago. Taken together, whole genome sequencing and local ancestry assignment therefore permit inferences about long-term histories of unsampled ancestral populations and highlights recent historical demographic processes that altered patterns of variation observed in admixed populations.

Analysis of the genomes of archaic hominins, such as Neandertals and Denisovans, has revealed that these groups have contributed to the genetic variation of modern human populations. Yet, we know little about how these ancient mixtures have shaped the genetic structure of human populations and even less about their impact on human evolution. To answer these questions systematically, we need a map of archaic ancestry i.e., a map that labels whether each region of an individual genome is descended from these archaics.

Building such a map is technically challenging because of the antiquity of these gene flow events. We have identified signatures based on patterns of variation at single SNPs as well as haplotypes that are informative of ancient gene flow.

We propose a principled method based on the statistical framework of Conditional Random Fields (CRFs) that integrates these patterns leading to highly accurate predictions. We applied our method to polymorphism data in European and East Asian individuals from the 1000 genomes project, in conjunction with the draft sequence of the Neandertal genome, to obtain the first genomewide map of Neandertal ancestry. Analysis of this map reveals several findings:

1. We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.

2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow.

3. Several of the Neandertal-derived alleles identified in 1) above are found in the >6,000 SNPs associated with common diseases listed in the NHGRI catalog. These Neandertal derived variants are found to be risk variants associated with obesity and protective variants against breast cancer.

4. We also investigate the possibility of using this map to reconstruct the genome of the introgressing Neandertal. Using the ancestries in Europe and East Asia, we can reconstruct about 600 Mb which we expect to increase with larger samples and additional populations.

The Etruscan culture is documented in Etruria, Central Italy, from the 7 th to the 1 st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals. Comparing ancient and modern diversity with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the modern inhabitants of two communities, Casentino and Volterra, but not to most contemporary populations dwelling in the former Etruscan homeland. We also estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, without a significant contribution of recent Anatolian immigrants.

Human population genomics in time and space: paleogenomics of populations in Bulgaria

With a few exceptions, most ancient human DNA studies to date have restricted their analysis to the mitochondrial DNA (mtDNA) and Y chromosome. These approaches have led to some interesting theories regarding the spread of human populations; however, they are inherently limited by their use of these two non-recombining markers, which are subject to forces such as genetic drift and natural selection and also represent only the histories of the female and male lines, respectively, from which they descend. Recently, the whole genomes of several ancient individuals have been sequenced. These genomes yielded much more information about the individuals’ ancestry than their mtDNA alone; nevertheless, a single ancient individual is not sufficient for population genetic analyses. Thus, the goal of our study is to sequence the genomes of multiple ancient individuals from the same population. This type of study has the potential to dramatically improve our ability to address demographic questions about ancient human populations. We have begun the low-coverage sequencing of genomic DNA from the teeth of 16 individuals from different time periods (1500 BC-400 BC) in Bulgaria, and we plan to ultimately extend the study to at least 50 ancient Bulgarian individuals from the Neolithic to the Iron Age (6300 BC-400 BC). The results of these initial experiments will be presented, including the identification of mtDNA haplogroups and initial population genetic analyses. Ultimately, we plan to analyze whole-genome sequence variation in these individuals and to compare it to variation present in modern populations. This will be the first systematic population-level study of ancient human genomes and therefore will allow us address demographic questions that have previously been restricted to the realm of theoretical modeling using extant populations.

The domestication of horse played a key role in human history. It seems to have happened far both in time and space from the domestication of other ungulates such as cattle, pig, sheep and goat. Archaeological studies, nevertheless, failed in determining exactly the region and modality for horse domestication: several centers have been proposed (at least one in Europe and one in Central Asia) and the relationship between wild and early domestic populations are not clear. From a genetic point of view a phylogenetic approach on modern mitochondrial diversity could not find any structure related with geography or breeds. In the last decade ancient DNA became an important tool to reconstruct past demography. We obtained more than 100 HVR I sequences from pre domestic and domestic specimens found in Europe and Central Asia. After collecting all the previously published ancient and modern comparable sequences from the sub mentioned regions, computer simulations with a Bayesian approach were performed in order to test demographic models related with single or multiple domestications with or without gene flow. A single domestication appears to be unrealistic on the basis of mitochondrial data, while possible model of multiple domestications will be discussed.

The complete mitochondrial genome of a third individual from Denisova Cave

A draft genome sequence was determined in 2010 from a small finger bone found in Denisova Cave in southern Siberia and was recently completed to 30-fold coverage. Its analysis reveals that it derived from an individual that belonged to a population related to, but distinct from, Neandertals. A large molar has also been described from Denisova Cave and shown to carry an mtDNA genome closely related to that of the finger bone. A second molar was found in Denisova Cave in 2010. We have captured and sequenced the complete mitochondrial genome of this tooth. While the mtDNAs of the finger bone and the first molar differ at only two nucleotide positions, they carry 86 and 84 differences, respectively, to the second molar. Thus, the maximum amount of mtDNA differences observed among these three Denisovans found within one cave is almost twice as large as the maximum differences seen among six Neandertals for which complete mtDNAs are available. Interestingly, the mtDNA of the second molar has a shorter branch than the other two Denisovan mtDNAs, suggesting that it may be older than the others.

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